data_5KUM # _model_server_result.job_id zU27pjXUY55S72hADU9zaw _model_server_result.datetime_utc '2024-10-18 21:29:35' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5kum # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5KUM # _exptl.entry_id 5KUM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 746.566 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5KUM _cell.length_a 81.303 _cell.length_b 81.303 _cell.length_c 183.572 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KUM _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 88 A CYS 123 1_555 A SG CYS 120 A CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 A O THR 108 A THR 143 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc2 A O THR 108 A THR 143 1_555 E K K . A K 404 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc3 A O THR 108 A THR 143 1_555 F K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc4 A OG1 THR 108 A THR 143 1_555 F K K . A K 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc5 A O THR 108 A THR 143 1_555 F K K . A K 405 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc6 A OG1 THR 108 A THR 143 1_555 F K K . A K 405 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc7 A O ILE 109 A ILE 144 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.102 ? metalc ? metalc8 A O ILE 109 A ILE 144 1_555 D K K . A K 403 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.102 ? metalc ? metalc9 A O ILE 109 A ILE 144 1_555 E K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.973 ? metalc ? metalc10 A O ILE 109 A ILE 144 1_555 E K K . A K 404 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.973 ? metalc ? metalc11 A O GLY 110 A GLY 145 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc12 A O GLY 110 A GLY 145 1_555 C K K . A K 402 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc13 A O GLY 110 A GLY 145 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc14 A O GLY 110 A GLY 145 1_555 D K K . A K 403 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc15 A O TYR 111 A TYR 146 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.089 ? metalc ? metalc16 A O TYR 111 A TYR 146 1_555 C K K . A K 402 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.089 ? # _chem_comp.formula 'C25 H49 O19 P3' _chem_comp.formula_weight 746.566 _chem_comp.id PIO _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 O1 PIO sing 336 n n C1 C2 PIO sing 337 n n C1 C6 PIO sing 338 n n C1 H1 PIO sing 339 n n O1 P1 PIO sing 340 n n P1 O11 PIO sing 341 n n O11 H11 PIO sing 342 n n P1 O12 PIO doub 343 n n P1 O13 PIO sing 344 n n C2 O2 PIO sing 345 n n C2 C3 PIO sing 346 n n C2 H2 PIO sing 347 n n O2 HO2 PIO sing 348 n n C3 O3 PIO sing 349 n n C3 C4 PIO sing 350 n n C3 H3 PIO sing 351 n n O3 HO3 PIO sing 352 n n C4 O4 PIO sing 353 n n C4 C5 PIO sing 354 n n C4 H4 PIO sing 355 n n O4 P4 PIO sing 356 n n P4 O41 PIO sing 357 n n O41 H41 PIO sing 358 n n P4 O42 PIO doub 359 n n P4 O43 PIO sing 360 n n O43 H43 PIO sing 361 n n C5 O5 PIO sing 362 n n C5 C6 PIO sing 363 n n C5 H5 PIO sing 364 n n O5 P5 PIO sing 365 n n P5 O51 PIO sing 366 n n O51 H51 PIO sing 367 n n P5 O52 PIO sing 368 n n O52 H52 PIO sing 369 n n P5 O53 PIO doub 370 n n C6 O6 PIO sing 371 n n C6 H6 PIO sing 372 n n O6 HO6 PIO sing 373 n n O13 C1C PIO sing 374 n n C1A O1A PIO doub 375 n n C1A C2A PIO sing 376 n n C1A O2C PIO sing 377 n n C1B O1B PIO doub 378 n n C1B C2B PIO sing 379 n n C1B O3C PIO sing 380 n n C1C C2C PIO sing 381 n n C1C H1C PIO sing 382 n n C1C H1CA PIO sing 383 n n C2A C3A PIO sing 384 n n C2A H2A PIO sing 385 n n C2A H2AA PIO sing 386 n n C2B C3B PIO sing 387 n n C2B H2B PIO sing 388 n n C2B H2BA PIO sing 389 n n C2C O2C PIO sing 390 n n C2C C3C PIO sing 391 n n C2C H2C PIO sing 392 n n C3A C4A PIO sing 393 n n C3A H3A PIO sing 394 n n C3A H3AA PIO sing 395 n n C3B C4B PIO sing 396 n n C3B H3B PIO sing 397 n n C3B H3BA PIO sing 398 n n C3C O3C PIO sing 399 n n C3C H3C PIO sing 400 n n C3C H3CA PIO sing 401 n n C4A C5A PIO sing 402 n n C4A H4A PIO sing 403 n n C4A H4AA PIO sing 404 n n C4B C5B PIO sing 405 n n C4B H4B PIO sing 406 n n C4B H4BA PIO sing 407 n n C5A C6A PIO sing 408 n n C5A H5A PIO sing 409 n n C5A H5AA PIO sing 410 n n C5B C6B PIO sing 411 n n C5B H5B PIO sing 412 n n C5B H5BA PIO sing 413 n n C6A C7A PIO sing 414 n n C6A H6A PIO sing 415 n n C6A H6AA PIO sing 416 n n C6B C7B PIO sing 417 n n C6B H6B PIO sing 418 n n C6B H6BA PIO sing 419 n n C7A C8A PIO sing 420 n n C7A H7A PIO sing 421 n n C7A H7AA PIO sing 422 n n C7B C8B PIO sing 423 n n C7B H7B PIO sing 424 n n C7B H7BA PIO sing 425 n n C8A H8A PIO sing 426 n n C8A H8AA PIO sing 427 n n C8A H8AB PIO sing 428 n n C8B H8B PIO sing 429 n n C8B H8BA PIO sing 430 n n C8B H8BB PIO sing 431 n n # _atom_sites.entry_id 5KUM _atom_sites.fract_transf_matrix[1][1] 0.0123 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0123 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.005447 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 PIO A 1 401 400 PIO PIO . C 3 K A 1 402 501 K K . D 3 K A 1 403 502 K K . E 3 K A 1 404 503 K K . F 3 K A 1 405 504 K K . G 3 K A 1 406 505 K K . H 3 K A 1 407 506 K K . I 3 K A 1 408 507 K K . J 3 K A 1 409 508 K K . K 4 DMU A 1 410 601 DMU DMU . L 5 HOH A 1 501 730 HOH HOH . L 5 HOH A 2 502 713 HOH HOH . L 5 HOH A 3 503 721 HOH HOH . L 5 HOH A 4 504 724 HOH HOH . L 5 HOH A 5 505 709 HOH HOH . L 5 HOH A 6 506 735 HOH HOH . L 5 HOH A 7 507 740 HOH HOH . L 5 HOH A 8 508 702 HOH HOH . L 5 HOH A 9 509 731 HOH HOH . L 5 HOH A 10 510 742 HOH HOH . L 5 HOH A 11 511 746 HOH HOH . L 5 HOH A 12 512 708 HOH HOH . L 5 HOH A 13 513 711 HOH HOH . L 5 HOH A 14 514 738 HOH HOH . L 5 HOH A 15 515 743 HOH HOH . L 5 HOH A 16 516 745 HOH HOH . L 5 HOH A 17 517 739 HOH HOH . L 5 HOH A 18 518 723 HOH HOH . L 5 HOH A 19 519 715 HOH HOH . L 5 HOH A 20 520 706 HOH HOH . L 5 HOH A 21 521 737 HOH HOH . L 5 HOH A 22 522 718 HOH HOH . L 5 HOH A 23 523 720 HOH HOH . L 5 HOH A 24 524 701 HOH HOH . L 5 HOH A 25 525 719 HOH HOH . L 5 HOH A 26 526 710 HOH HOH . L 5 HOH A 27 527 703 HOH HOH . L 5 HOH A 28 528 707 HOH HOH . L 5 HOH A 29 529 727 HOH HOH . L 5 HOH A 30 530 733 HOH HOH . L 5 HOH A 31 531 722 HOH HOH . L 5 HOH A 32 532 736 HOH HOH . L 5 HOH A 33 533 734 HOH HOH . L 5 HOH A 34 534 741 HOH HOH . L 5 HOH A 35 535 732 HOH HOH . L 5 HOH A 36 536 714 HOH HOH . L 5 HOH A 37 537 747 HOH HOH . L 5 HOH A 38 538 716 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 PIO . . . B 2 -19.612 -9.583 -9.981 1 99.76 ? C1 PIO 401 A 1 HETATM 2 O O1 PIO . . . B 2 -20 -8.807 -11.137 1 87.24 ? O1 PIO 401 A 1 HETATM 3 P P1 PIO . . . B 2 -20.179 -9.416 -12.636 1 81.55 ? P1 PIO 401 A 1 HETATM 4 C C2 PIO . . . B 2 -20.667 -10.645 -9.562 1 108.84 ? C2 PIO 401 A 1 HETATM 5 O O2 PIO . . . B 2 -21.985 -10.181 -9.868 1 115.97 ? O2 PIO 401 A 1 HETATM 6 C C3 PIO . . . B 2 -20.702 -11.038 -8.078 1 111.91 ? C3 PIO 401 A 1 HETATM 7 O O3 PIO . . . B 2 -21.893 -11.78 -7.809 1 113.59 ? O3 PIO 401 A 1 HETATM 8 C C4 PIO . . . B 2 -20.669 -9.762 -7.243 1 116.35 ? C4 PIO 401 A 1 HETATM 9 O O4 PIO . . . B 2 -21.007 -9.863 -5.836 1 124.35 ? O4 PIO 401 A 1 HETATM 10 P P4 PIO . . . B 2 -20.426 -10.846 -4.684 1 128.15 ? P4 PIO 401 A 1 HETATM 11 C C5 PIO . . . B 2 -19.286 -9.174 -7.494 1 108.22 ? C5 PIO 401 A 1 HETATM 12 O O5 PIO . . . B 2 -18.986 -8.214 -6.489 1 97.64 ? O5 PIO 401 A 1 HETATM 13 P P5 PIO . . . B 2 -17.476 -7.728 -6.301 1 87.64 ? P5 PIO 401 A 1 HETATM 14 C C6 PIO . . . B 2 -19.279 -8.56 -8.895 1 100.64 ? C6 PIO 401 A 1 HETATM 15 O O6 PIO . . . B 2 -18.012 -7.981 -9.207 1 92.84 ? O6 PIO 401 A 1 HETATM 16 O O11 PIO . . . B 2 -21.521 -10.106 -12.682 1 84.86 ? O11 PIO 401 A 1 HETATM 17 O O12 PIO . . . B 2 -20.038 -8.307 -13.644 1 77.5 ? O12 PIO 401 A 1 HETATM 18 O O13 PIO . . . B 2 -18.951 -10.511 -12.765 1 73.17 ? O13 PIO 401 A 1 HETATM 19 C C1C PIO . . . B 2 -18.381 -10.946 -14.022 1 70.46 ? C1C PIO 401 A 1 HETATM 20 C C2C PIO . . . B 2 -16.892 -11.298 -13.927 1 67.06 ? C2C PIO 401 A 1 HETATM 21 O O41 PIO . . . B 2 -21.562 -11.827 -4.517 1 126.37 ? O41 PIO 401 A 1 HETATM 22 O O42 PIO . . . B 2 -19.157 -11.488 -5.214 1 115.19 ? O42 PIO 401 A 1 HETATM 23 O O43 PIO . . . B 2 -20.241 -9.919 -3.5 1 104.82 ? O43 PIO 401 A 1 HETATM 24 O O51 PIO . . . B 2 -16.557 -8.805 -6.863 1 77.53 ? O51 PIO 401 A 1 HETATM 25 O O52 PIO . . . B 2 -17.331 -7.549 -4.81 1 82.68 ? O52 PIO 401 A 1 HETATM 26 O O53 PIO . . . B 2 -17.552 -6.461 -7.118 1 85.09 ? O53 PIO 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #